Iron in the structure of Crystal Structure Of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture. (pdb 3d38)

The binding sites of Iron atom in the structure of Crystal Structure Of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture. (pdb code 3d38). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3d38 structure was solved by L.LI, S.H.M.NACHTERGAELE, A.M.SEDDON, V.TERESHKO, N.PONOMARENKO, R.F.ISMAGILOV, ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3DSTRUCTURE (ATCG3D), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:

Resolution (A)

50.0-3.2

Space group

P3121

a (A)

241.171

b (A)

241.171

c (A)

113.391

alpha (°)

90.00

beta (°)

90.00

gamma (°)

120.00

Rfactor (%)

19.2

Rfree (%)

22.4

Iron Binding Sites:

Iron binding site 1 out of 5 in 3d38

Click to enlarge

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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3d38. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: C: Met74, C: His91, C: Hec401,

conact list:

Atom

Atom

Distance (A)

Fe

CB C:Met74

4.32

Fe

CE C:Met74

3.31

Fe

CG C:Met74

3.61

Fe

SD C:Met74

2.25

Fe

NE2 C:His91

1.98

Fe

ND1 C:His91

3.89

Fe

CD2 C:His91

3.20

Fe

CE1 C:His91

2.67

Fe

CG C:His91

4.17

Fe

C2D C:Hec401

4.23

Fe

NC C:Hec401

2.04

Fe

CHB C:Hec401

3.45

Fe

CHC C:Hec401

3.47

Fe

C3D C:Hec401

4.24

Fe

NA C:Hec401

2.03

Fe

CHA C:Hec401

3.40

Fe

C2A C:Hec401

4.24

Fe

C1D C:Hec401

3.03

Fe

C4A C:Hec401

3.05

Fe

C4B C:Hec401

3.12

Fe

C3A C:Hec401

4.25

Fe

C4C C:Hec401

3.04

Fe

C2B C:Hec401

4.34

Fe

C1C C:Hec401

3.09

Fe

C2C C:Hec401

4.30

Fe

ND C:Hec401

2.05

Fe

CHD C:Hec401

3.39

Fe

C1B C:Hec401

3.11

Fe

NB C:Hec401

2.10

Fe

FE C:Hec401

0.00

Fe

C3C C:Hec401

4.27

Fe

C3B C:Hec401

4.35

Fe

C4D C:Hec401

3.04

Fe

C1A C:Hec401

3.03

interactive model:

Iron binding site 2 out of 5 in 3d38

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3d38. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: C: Met110, C: His136, C: Hec402,

conact list:

Atom

Atom

Distance (A)

Fe

CB C:Met110

4.24

Fe

CE C:Met110

3.52

Fe

CG C:Met110

3.51

Fe

SD C:Met110

2.31

Fe

NE2 C:His136

1.95

Fe

ND1 C:His136

3.96

Fe

CD2 C:His136

3.06

Fe

CE1 C:His136

2.79

Fe

CG C:His136

4.11

Fe

C2D C:Hec402

4.29

Fe

NC C:Hec402

2.05

Fe

CHB C:Hec402

3.42

Fe

CHC C:Hec402

3.40

Fe

C3D C:Hec402

4.29

Fe

NA C:Hec402

2.08

Fe

CHA C:Hec402

3.47

Fe

C2A C:Hec402

4.30

Fe

C1D C:Hec402

3.07

Fe

C4A C:Hec402

3.07

Fe

C4B C:Hec402

3.02

Fe

C3A C:Hec402

4.28

Fe

C4C C:Hec402

3.09

Fe

C2B C:Hec402

4.21

Fe

C1C C:Hec402

3.05

Fe

C2C C:Hec402

4.29

Fe

ND C:Hec402

2.06

Fe

CHD C:Hec402

3.45

Fe

C1B C:Hec402

3.02

Fe

NB C:Hec402

2.01

Fe

FE C:Hec402

0.00

Fe

C3C C:Hec402

4.31

Fe

C3B C:Hec402

4.21

Fe

C4D C:Hec402

3.09

Fe

C1A C:Hec402

3.10

interactive model:

Iron binding site 3 out of 5 in 3d38

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3d38. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: C: Met233, C: His248, C: Hec403,